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- PDB-7f09: Crystal structure of the HLH-Lz domain of human TFE3 -

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Basic information

Entry
Database: PDB / ID: 7f09
TitleCrystal structure of the HLH-Lz domain of human TFE3
ComponentsTranscription factor E3
KeywordsTRANSCRIPTION / Transcription factor E3 / HLH-Lz domain
Function / homology
Function and homology information


regulation of osteoclast differentiation / negative regulation of cold-induced thermogenesis / humoral immune response / positive regulation of cell adhesion / positive regulation of brown fat cell differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / adaptive immune response / protein dimerization activity / transcription cis-regulatory region binding ...regulation of osteoclast differentiation / negative regulation of cold-induced thermogenesis / humoral immune response / positive regulation of cell adhesion / positive regulation of brown fat cell differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / adaptive immune response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor E3 / MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Transcription factor E3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, G. / Li, P. / Liu, Z. / Wu, S. / Zhuang, C. / Qiao, H. / Fang, P. / Wang, J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977107 China
National Natural Science Foundation of China (NSFC)21977108 China
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21778064 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis for the dimerization mechanism of human transcription factor E3.
Authors: Yang, G. / Li, P. / Liu, Z. / Wu, S. / Zhuang, C. / Qiao, H. / Zheng, L. / Fang, P. / Lei, C. / Wang, J.
History
DepositionJun 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor E3
B: Transcription factor E3
C: Transcription factor E3
D: Transcription factor E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26816
Polymers34,5034
Non-polymers76512
Water93752
1
A: Transcription factor E3
B: Transcription factor E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6348
Polymers17,2522
Non-polymers3826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-106 kcal/mol
Surface area9530 Å2
MethodPISA
2
C: Transcription factor E3
D: Transcription factor E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6348
Polymers17,2522
Non-polymers3826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-57 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.940, 47.370, 69.960
Angle α, β, γ (deg.)85.240, 87.210, 88.320
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Transcription factor E3 / Class E basic helix-loop-helix protein 33 / bHLHe33


Mass: 8625.815 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFE3, BHLHE33 / Production host: Escherichia coli (E. coli) / References: UniProt: P19532
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Zinc Acetate, Zinc Chloride, Bis-Tris pH 7.5, PEG 3350, PEG 2000, PEG 4000 and PEG 5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→47.19 Å / Num. obs: 17459 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.721.80.253231612990.9130.2520.3573.297.1
9.01-47.191.70.0273652180.9970.0270.03819.883.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KU4

6ku4
PDB Unreleased entry


Resolution: 2.6→18.833 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.41 / Phase error: 31.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 863 4.94 %
Rwork0.2208 16594 -
obs0.2219 17457 79.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.48 Å2 / Biso mean: 71.8898 Å2 / Biso min: 30.72 Å2
Refinement stepCycle: final / Resolution: 2.6→18.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 30 52 2129
Biso mean--93.56 77.02 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.76260.32791490.276280981
2.7626-2.97510.32521630.2711283582
2.9751-3.27310.3521390.2545273479
3.2731-3.74350.22061680.2351270679
3.7435-4.70420.19231200.1875287981
4.7042-18.8330.23191240.21263176
Refinement TLS params.Method: refined / Origin x: -0.5596 Å / Origin y: 4.0699 Å / Origin z: 6.6314 Å
111213212223313233
T0.4072 Å20.0061 Å2-0.0111 Å2-0.4354 Å2-0.0077 Å2--0.394 Å2
L-0.2737 °20.0975 °20.0282 °2--0.0094 °20.3872 °2--0.4022 °2
S-0.0365 Å °-0.0343 Å °-0.0137 Å °0.071 Å °0.0241 Å °0.0157 Å °0.0665 Å °0.0461 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA359 - 432
2X-RAY DIFFRACTION1allB359 - 432
3X-RAY DIFFRACTION1allC359 - 431
4X-RAY DIFFRACTION1allD359 - 431
5X-RAY DIFFRACTION1allE1 - 6
6X-RAY DIFFRACTION1allF1 - 52
7X-RAY DIFFRACTION1allG1 - 6

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